Name: rs16825685
Published: September 21, 2022
License: Open Access

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs16825685

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr2:224569539 (GRCh38.p14) Help
The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.
Alleles: C>A / C>G / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.299244 (79207/264690, TOPMED)
G=0.33490 (9463/28256, 14KJPN)
G=0.33675 (5644/16760, 8.3KJPN) (+ 17 more)
G=0.18792 (2387/12702, ALFA)
G=0.2895 (1854/6404, 1000G_30x)
G=0.2931 (1468/5008, 1000G)
G=0.3531 (1582/4480, Estonian)
G=0.3168 (1221/3854, ALSPAC)
G=0.3201 (1187/3708, TWINSUK)
G=0.2410 (706/2930, KOREAN)
G=0.2533 (464/1832, Korea1K)
G=0.325 (324/998, GoNL)
G=0.380 (228/600, NorthernSweden)
G=0.015 (8/534, MGP)
C=0.382 (113/296, SGDP_PRJ)
G=0.361 (78/216, Qatari)
G=0.421 (91/216, Vietnamese)
G=0.33 (13/40, GENOME_DK)
C=0.50 (9/18, Siberian)
G=0.50 (9/18, Siberian)

Clinical Significance: Reported in ClinVar
Gene : Consequence: CUL3 : Intron Variant
Publications: 0 citations
Genomic View: See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	12702	C=0.81208	A=0.00000, G=0.18792, T=0.00000	0.690442	0.066289	0.243269	32
European	Sub	9972	C=0.7706	A=0.0000, G=0.2294, T=0.0000	0.623145	0.08203	0.294826	32
African	Sub	1872	C=0.9850	A=0.0000, G=0.0150, T=0.0000	0.973291	0.003205	0.023504	21
African Others	Sub	78	C=0.99	A=0.00, G=0.01, T=0.00	0.974359	0.0	0.025641	0
African American	Sub	1794	C=0.9849	A=0.0000, G=0.0151, T=0.0000	0.973244	0.003344	0.023411	21
Asian	Sub	52	C=1.00	A=0.00, G=0.00, T=0.00	1.0	0.0	0.0	N/A
East Asian	Sub	38	C=1.00	A=0.00, G=0.00, T=0.00	1.0	0.0	0.0	N/A
Other Asian	Sub	14	C=1.00	A=0.00, G=0.00, T=0.00	1.0	0.0	0.0	N/A
Latin American 1	Sub	60	C=1.00	A=0.00, G=0.00, T=0.00	1.0	0.0	0.0	N/A
Latin American 2	Sub	236	C=1.000	A=0.000, G=0.000, T=0.000	1.0	0.0	0.0	N/A
South Asian	Sub	54	C=0.98	A=0.00, G=0.02, T=0.00	0.962963	0.0	0.037037	0
Other	Sub	456	C=0.846	A=0.000, G=0.154, T=0.000	0.732456	0.039474	0.22807	2

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	C=0.700756	G=0.299244
14KJPN	JAPANESE	Study-wide	28256	C=0.66510	G=0.33490
8.3KJPN	JAPANESE	Study-wide	16760	C=0.66325	G=0.33675
Allele Frequency Aggregator	Total	Global	12702	C=0.81208	A=0.00000, G=0.18792, T=0.00000
Allele Frequency Aggregator	European	Sub	9972	C=0.7706	A=0.0000, G=0.2294, T=0.0000
Allele Frequency Aggregator	African	Sub	1872	C=0.9850	A=0.0000, G=0.0150, T=0.0000
Allele Frequency Aggregator	Other	Sub	456	C=0.846	A=0.000, G=0.154, T=0.000
Allele Frequency Aggregator	Latin American 2	Sub	236	C=1.000	A=0.000, G=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	60	C=1.00	A=0.00, G=0.00, T=0.00
Allele Frequency Aggregator	South Asian	Sub	54	C=0.98	A=0.00, G=0.02, T=0.00
Allele Frequency Aggregator	Asian	Sub	52	C=1.00	A=0.00, G=0.00, T=0.00
1000Genomes_30x	Global	Study-wide	6404	C=0.7105	G=0.2895
1000Genomes_30x	African	Sub	1786	C=0.7928	G=0.2072
1000Genomes_30x	Europe	Sub	1266	C=0.6769	G=0.3231
1000Genomes_30x	South Asian	Sub	1202	C=0.7554	G=0.2446
1000Genomes_30x	East Asian	Sub	1170	C=0.6342	G=0.3658
1000Genomes_30x	American	Sub	980	C=0.640	G=0.360
1000Genomes	Global	Study-wide	5008	C=0.7069	G=0.2931
1000Genomes	African	Sub	1322	C=0.7973	G=0.2027
1000Genomes	East Asian	Sub	1008	C=0.6349	G=0.3651
1000Genomes	Europe	Sub	1006	C=0.6700	G=0.3300
1000Genomes	South Asian	Sub	978	C=0.742	G=0.258
1000Genomes	American	Sub	694	C=0.643	G=0.357
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.6469	G=0.3531
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.6832	G=0.3168
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.6799	G=0.3201
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.7590	G=0.2410
Korean Genome Project	KOREAN	Study-wide	1832	C=0.7467	G=0.2533
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.675	G=0.325
Northern Sweden	ACPOP	Study-wide	600	C=0.620	G=0.380
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	C=0.985	G=0.015
SGDP_PRJ	Global	Study-wide	296	C=0.382	G=0.618
Qatari	Global	Study-wide	216	C=0.639	G=0.361
A Vietnamese Genetic Variation Database	Global	Study-wide	216	C=0.579	G=0.421
The Danish reference pan genome	Danish	Study-wide	40	C=0.68	G=0.33
Siberian	Global	Study-wide	18	C=0.50	G=0.50

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements

Sequence name	Change
GRCh38.p14 chr 2	NC_000002.12:g.224569539C>A
GRCh38.p14 chr 2	NC_000002.12:g.224569539C>G
GRCh38.p14 chr 2	NC_000002.12:g.224569539C>T
GRCh37.p13 chr 2	NC_000002.11:g.225434256C>A
GRCh37.p13 chr 2	NC_000002.11:g.225434256C>G
GRCh37.p13 chr 2	NC_000002.11:g.225434256C>T
CUL3 RefSeqGene	NG_032169.1:g.20859G>T
CUL3 RefSeqGene	NG_032169.1:g.20859G>C
CUL3 RefSeqGene	NG_032169.1:g.20859G>A

Gene: CUL3, cullin 3 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CUL3 transcript variant 2	NM_001257197.2:c.66+15405… NM_001257197.2:c.66+15405G>T	N/A	Intron Variant
CUL3 transcript variant 3	NM_001257198.2:c.84+150G>T	N/A	Intron Variant
CUL3 transcript variant 1	NM_003590.5:c.67-11683G>T	N/A	Intron Variant
CUL3 transcript variant X1	XM_006712800.3:c.	N/A	Genic Upstream Transcript Variant
CUL3 transcript variant X2	XM_011511995.2:c.	N/A	Genic Upstream Transcript Variant
CUL3 transcript variant X3	XM_011511996.3:c.	N/A	Genic Upstream Transcript Variant
CUL3 transcript variant X4	XM_047446024.1:c.	N/A	Genic Upstream Transcript Variant

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Allele: G (allele ID: 1236076 )

ClinVar Accession	Disease Names	Clinical Significance
RCV001649047.2	not provided	Benign

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement	C=	A	G	T
GRCh38.p14 chr 2	NC_000002.12:g.224569539=	NC_000002.12:g.224569539C>A	NC_000002.12:g.224569539C>G	NC_000002.12:g.224569539C>T
GRCh37.p13 chr 2	NC_000002.11:g.225434256=	NC_000002.11:g.225434256C>A	NC_000002.11:g.225434256C>G	NC_000002.11:g.225434256C>T
CUL3 RefSeqGene	NG_032169.1:g.20859=	NG_032169.1:g.20859G>T	NG_032169.1:g.20859G>C	NG_032169.1:g.20859G>A
CUL3 transcript variant 2	NM_001257197.1:c.66+15405=	NM_001257197.1:c.66+15405G>T	NM_001257197.1:c.66+15405G>C	NM_001257197.1:c.66+15405G>A
CUL3 transcript variant 2	NM_001257197.2:c.66+15405=	NM_001257197.2:c.66+15405G>T	NM_001257197.2:c.66+15405G>C	NM_001257197.2:c.66+15405G>A
CUL3 transcript variant 3	NM_001257198.1:c.84+150=	NM_001257198.1:c.84+150G>T	NM_001257198.1:c.84+150G>C	NM_001257198.1:c.84+150G>A
CUL3 transcript variant 3	NM_001257198.2:c.84+150=	NM_001257198.2:c.84+150G>T	NM_001257198.2:c.84+150G>C	NM_001257198.2:c.84+150G>A
CUL3 transcript variant 1	NM_003590.4:c.67-11683=	NM_003590.4:c.67-11683G>T	NM_003590.4:c.67-11683G>C	NM_003590.4:c.67-11683G>A
CUL3 transcript variant 1	NM_003590.5:c.67-11683=	NM_003590.5:c.67-11683G>T	NM_003590.5:c.67-11683G>C	NM_003590.5:c.67-11683G>A

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

63 SubSNP, 21 Frequency, 1 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	PERLEGEN	ss23711716	Sep 20, 2004 (123)
2	1000GENOMES	ss110853652	Jan 25, 2009 (130)
3	GMI	ss154785943	Dec 01, 2009 (131)
4	COMPLETE_GENOMICS	ss165934754	Jul 04, 2010 (132)
5	BUSHMAN	ss201810751	Jul 04, 2010 (132)
6	BCM-HGSC-SUB	ss205887448	Jul 04, 2010 (132)
7	1000GENOMES	ss211095414	Jul 14, 2010 (132)
8	1000GENOMES	ss219844387	Jul 14, 2010 (132)
9	1000GENOMES	ss231608465	Jul 14, 2010 (132)
10	1000GENOMES	ss239062590	Jul 15, 2010 (132)
11	GMI	ss276918989	May 04, 2012 (137)
12	TISHKOFF	ss556259434	Apr 25, 2013 (138)
13	SSMP	ss649922844	Apr 25, 2013 (138)
14	EVA-GONL	ss978018538	Aug 21, 2014 (142)
15	JMKIDD_LAB	ss1069984596	Aug 21, 2014 (142)
16	1000GENOMES	ss1301868424	Aug 21, 2014 (142)
17	DDI	ss1428928535	Apr 01, 2015 (144)
18	EVA_GENOME_DK	ss1579345985	Apr 01, 2015 (144)
19	EVA_DECODE	ss1587475750	Apr 01, 2015 (144)
20	EVA_UK10K_ALSPAC	ss1605914654	Apr 01, 2015 (144)
21	EVA_UK10K_TWINSUK	ss1648908687	Apr 01, 2015 (144)
22	EVA_MGP	ss1710998594	Apr 01, 2015 (144)
23	HAMMER_LAB	ss1798452523	Sep 08, 2015 (146)
24	WEILL_CORNELL_DGM	ss1921263719	Feb 12, 2016 (147)
25	GENOMED	ss1969039636	Jul 19, 2016 (147)
26	JJLAB	ss2021180300	Sep 14, 2016 (149)
27	USC_VALOUEV	ss2149244506	Dec 20, 2016 (150)
28	HUMAN_LONGEVITY	ss2239619063	Dec 20, 2016 (150)
29	SYSTEMSBIOZJU	ss2625090760	Nov 08, 2017 (151)
30	GRF	ss2703893985	Nov 08, 2017 (151)
31	GNOMAD	ss2786957811	Nov 08, 2017 (151)
32	SWEGEN	ss2991447750	Nov 08, 2017 (151)
33	BIOINF_KMB_FNS_UNIBA	ss3024348969	Nov 08, 2017 (151)
34	CSHL	ss3344766232	Nov 08, 2017 (151)
35	EGCUT_WGS	ss3659346314	Jul 13, 2019 (153)
36	EVA_DECODE	ss3706133440	Jul 13, 2019 (153)
37	ACPOP	ss3729420627	Jul 13, 2019 (153)
38	EVA	ss3758153714	Jul 13, 2019 (153)
39	PACBIO	ss3784169924	Jul 13, 2019 (153)
40	PACBIO	ss3789705678	Jul 13, 2019 (153)
41	PACBIO	ss3794578932	Jul 13, 2019 (153)
42	KHV_HUMAN_GENOMES	ss3802516074	Jul 13, 2019 (153)
43	EVA	ss3827534623	Apr 25, 2020 (154)
44	EVA	ss3837187113	Apr 25, 2020 (154)
45	EVA	ss3842609330	Apr 25, 2020 (154)
46	SGDP_PRJ	ss3854711415	Apr 25, 2020 (154)
47	KRGDB	ss3900442185	Apr 25, 2020 (154)
48	KOGIC	ss3950197199	Apr 25, 2020 (154)
49	TOPMED	ss4546579090	Apr 26, 2021 (155)
50	TOMMO_GENOMICS	ss5156747904	Apr 26, 2021 (155)
51	1000G_HIGH_COVERAGE	ss5252225754	Oct 12, 2022 (156)
52	EVA	ss5336398392	Oct 12, 2022 (156)
53	HUGCELL_USP	ss5451820393	Oct 12, 2022 (156)
54	EVA	ss5506815581	Oct 12, 2022 (156)
55	1000G_HIGH_COVERAGE	ss5529672424	Oct 12, 2022 (156)
56	SANFORD_IMAGENETICS	ss5631063402	Oct 12, 2022 (156)
57	TOMMO_GENOMICS	ss5687705045	Oct 12, 2022 (156)
58	YY_MCH	ss5803269204	Oct 12, 2022 (156)
59	EVA	ss5821668395	Oct 12, 2022 (156)
60	EVA	ss5852974734	Oct 12, 2022 (156)
61	EVA	ss5934933463	Oct 12, 2022 (156)
62	EVA	ss5957324690	Oct 12, 2022 (156)
63	EVA	ss5980115655	Oct 12, 2022 (156)
64	1000Genomes	NC_000002.11 - 225434256	Oct 11, 2018 (152)
65	1000Genomes_30x	NC_000002.12 - 224569539	Oct 12, 2022 (156)
66	The Avon Longitudinal Study of Parents and Children	NC_000002.11 - 225434256	Oct 11, 2018 (152)
67	Genetic variation in the Estonian population	NC_000002.11 - 225434256	Oct 11, 2018 (152)
68	The Danish reference pan genome	NC_000002.11 - 225434256	Apr 25, 2020 (154)
69	gnomAD - Genomes Submission ignored due to conflicting rows: Row 92535694 (NC_000002.12:224569538:C:A 1/139992) Row 92535695 (NC_000002.12:224569538:C:G 41544/139940)	-	Apr 26, 2021 (155)
70	gnomAD - Genomes Submission ignored due to conflicting rows: Row 92535694 (NC_000002.12:224569538:C:A 1/139992) Row 92535695 (NC_000002.12:224569538:C:G 41544/139940)	-	Apr 26, 2021 (155)
71	Genome of the Netherlands Release 5	NC_000002.11 - 225434256	Apr 25, 2020 (154)
72	KOREAN population from KRGDB	NC_000002.11 - 225434256	Apr 25, 2020 (154)
73	Korean Genome Project	NC_000002.12 - 224569539	Apr 25, 2020 (154)
74	Medical Genome Project healthy controls from Spanish population	NC_000002.11 - 225434256	Apr 25, 2020 (154)
75	Northern Sweden	NC_000002.11 - 225434256	Jul 13, 2019 (153)
76	Qatari	NC_000002.11 - 225434256	Apr 25, 2020 (154)
77	SGDP_PRJ	NC_000002.11 - 225434256	Apr 25, 2020 (154)
78	Siberian	NC_000002.11 - 225434256	Apr 25, 2020 (154)
79	8.3KJPN	NC_000002.11 - 225434256	Apr 26, 2021 (155)
80	14KJPN	NC_000002.12 - 224569539	Oct 12, 2022 (156)
81	TopMed	NC_000002.12 - 224569539	Apr 26, 2021 (155)
82	UK 10K study - Twins	NC_000002.11 - 225434256	Oct 11, 2018 (152)
83	A Vietnamese Genetic Variation Database	NC_000002.11 - 225434256	Jul 13, 2019 (153)
84	ALFA	NC_000002.12 - 224569539	Apr 26, 2021 (155)
85	ClinVar	RCV001649047.2	Oct 12, 2022 (156)

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss2786957811	NC_000002.11:225434255:C:A	NC_000002.12:224569538:C:A	(self)
11641253501	NC_000002.12:224569538:C:A	NC_000002.12:224569538:C:A	(self)
ss110853652, ss165934754, ss201810751, ss205887448, ss211095414, ss276918989, ss1587475750	NC_000002.10:225142499:C:G	NC_000002.12:224569538:C:G	(self)
12981777, 7184966, 5084562, 5510924, 3149350, 7619579, 115133, 2705492, 3305649, 6728395, 1760860, 14717211, 7184966, 1561285, ss219844387, ss231608465, ss239062590, ss556259434, ss649922844, ss978018538, ss1069984596, ss1301868424, ss1428928535, ss1579345985, ss1605914654, ss1648908687, ss1710998594, ss1798452523, ss1921263719, ss1969039636, ss2021180300, ss2149244506, ss2625090760, ss2703893985, ss2786957811, ss2991447750, ss3344766232, ss3659346314, ss3729420627, ss3758153714, ss3784169924, ss3789705678, ss3794578932, ss3827534623, ss3837187113, ss3854711415, ss3900442185, ss5156747904, ss5336398392, ss5506815581, ss5631063402, ss5821668395, ss5957324690, ss5980115655	NC_000002.11:225434255:C:G	NC_000002.12:224569538:C:G	(self)
RCV001649047.2, 17198359, 6575200, 21542149, 350401969, 11641253501, ss2239619063, ss3024348969, ss3706133440, ss3802516074, ss3842609330, ss3950197199, ss4546579090, ss5252225754, ss5451820393, ss5529672424, ss5687705045, ss5803269204, ss5852974734, ss5934933463	NC_000002.12:224569538:C:G	NC_000002.12:224569538:C:G	(self)
ss23711716, ss154785943	NT_005403.17:75643673:C:G	NC_000002.12:224569538:C:G	(self)
11641253501	NC_000002.12:224569538:C:T	NC_000002.12:224569538:C:T	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs16825685

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:

Select flank length:

Genomic regions, transcripts, and products
Top▲ Help
NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs16825685